Amber users,
I am trying to run MD of a 53,059 atom system with a restraint on part
of the protein. I solvated using a cap around the area of interest, and
tried to run MD using igb = 10, which calculates a reaction field for
the system, and the run crashes. Alternatively, this same system works
fine with Generalized Born (igb = 1).
I get the following error with igb = 10:
4. RESULTS
--------------------------------------------------------------------------------
PB bomb in pb_reslist(): maxnbr too small
According to a previous post, this error could be fixed by increasing
the cutres. When I add "cutres" to the input file to increase it from
the default of 12 to a value of 15, the run immediately crashes and I
get the following error:
PGFIO-F-239/namelist read/unit=5/entity name is not member of group.
File name = initialMD.in formatted, sequential access record = 11
In source file _mdread.f, at line number 1088
Has anyone experienced a similar error?
Thank you!
Rachel Burdge
Washington University in St. Louis
Here is my complete output file:
-------------------------------------------------------
Amber 8 SANDER Scripps/UCSF 2004
-------------------------------------------------------
| Run on 02/10/2005 at 09:54:55
[-O]verwriting output
File Assignments:
| MDIN: initialMD.in
| MDOUT: initialMD.out
|INPCRD: start.crd
| PARM: start.top
|RESTRT: restrt
| REFC: start.crd
| MDVEL: mdvel
| MDEN: mden
| MDCRD: mdcrd
|MDINFO: initialMD.info
|INPDIP: inpdip
|RSTDIP: rstdip
Here is the input file:
MD of solvent only, 50K, 10ps, 1fs step, no shake, npt
&cntrl
nmropt = 0,
ntx = 1, irest = 0, ntrx = 1, ntxo = 1,
ntpr = 50, ntwx = 500, ntwv = 0, ntwe = 0,
ntf = 1, ntb = 0,
cut = 40.0, nsnb = 10,
ibelly = 0, ntr = 1, igb = 10,
restraintmask = ':* & !:2855<:20.0 & !:WAT',
restraint_wt = 10,
imin = 0,
nstlim = 10000,
nscm = 0,
t = 0.0, dt = 0.001,
temp0 = 50.0, tempi = 50.0,
ig = 71277, heat = 0.0,
ntt = 1,
tautp = 0.2,
vrand = 50,
vlimit = 15.0,
ntp = 0, pres0 = 1.0, comp = 44.6,
taup = 0.2, npscal = 1,
ntc = 1, tol = 0.00001,
&end
-------------------------------------------------------------------------------- 1. RESOURCE USE:
--------------------------------------------------------------------------------
Warning: heat has been retired.
Check the Retired Namelist Variables Appendix in the manual.
| Flags: MPI
| New format PARM file being parsed.
| Version = 1.000 Date = 02/08/05 Time = 13:16:17
NATOM = 53059 NTYPES = 19 NBONH = 29806 MBONA = 23838
NTHETH = 51387 MTHETA = 32519 NPHIH = 96811 MPHIA = 60226
NHPARM = 0 NPARM = 0 NNB = 262835 NRES = 5254
NBONA = 23838 NTHETA = 32519 NPHIA = 60226 NUMBND = 74
NUMANG = 166 NPTRA = 66 NATYP = 39 NPHB = 1
IFBOX = 0 NMXRS = 33 IFCAP = 1 NEXTRA = 0
NCOPY = 0
| Memory Use Allocated
| Real 1699784
| Hollerith 323610
| Integer 2475577
| Max Pairs 1
| Max Rstack 1
| Max Istack 1
| Total 24213 kbytes
| Duplicated 0 dihedrals
| Duplicated 0 dihedrals
-------------------------------------------------------------------------------- 2. CONTROL DATA FOR THE RUN
--------------------------------------------------------------------------------
General flags:
imin = 0, nmropt = 0
Nature and format of input:
ntx = 1, irest = 0, ntrx = 1
Nature and format of output:
ntxo = 1, ntpr = 50, ntrx = 1, ntwr
= 500
iwrap = 0, ntwx = 500, ntwv = 0, ntwe
= 0
ioutfm = 0, ntwprt = 0, idecomp = 0,
rbornstat= 0
Potential function:
ntf = 1, ntb = 0, igb = 10, nsnb
= 10
ipol = 0, gbsa = 0, iesp = 0
dielc = 1.00000, cut = 40.00000, intdiel = 1.00000
scnb = 2.00000, scee = 1.20000
Frozen or restrained atoms:
ibelly = 0, ntr = 1
Molecular dynamics:
nstlim = 10000, nscm = 9999999, nrespa = 1
t = 0.00000, dt = 0.00100, vlimit = 15.00000
Berendsen (weak-coupling) temperature regulation:
temp0 = 50.00000, tempi = 50.00000, tautp = 0.20000
Water cap:
ivcap = 0, natcap = 45862
fcap = 1.50000, cutcap = 50.00000
xcap = 76.00000, ycap = 93.00000, zcap = 44.00000
LOADING THE CONSTRAINED ATOMS AS GROUPS
5. REFERENCE ATOM COORDINATES
Mask :* & !:2855<:20.0 & !:WAT; matches 40729 atoms
-------------------------------------------------------------------------------- 3. ATOMIC COORDINATES AND VELOCITIES
--------------------------------------------------------------------------------
begin time read from input coords = 0.000 ps
Number of triangulated 3-point waters found: 2399
| Atom division among processors:
| 0 26534 53059
| Running AMBER/MPI version on 2 nodes
-------------------------------------------------------------------------------- 4. RESULTS
--------------------------------------------------------------------------------
PB bomb in pb_reslist(): maxnbr too small
(END)
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Received on Thu Feb 10 2005 - 16:53:00 PST
